Characteristics of heavy metals in sediments from different sources are significant varied,which impact on the degree of damage for aquatic system. Samples from municipal, mining, industrial and port sources in the lower reaches of the Yangtze River were analyzed for major elements and Cu, Zn, Pb, Cd, Cr by ICP-AES and AAS. The results showed that the concentrations were moderately and relatively uniform for heavy metals in the municipal source, Cu, Pb were dominated for the mine source. Five metals had higher concentrations in industrial source, and Cd was the highest in sediments from port source. The enrichment factors of heavy metals in sediments were high, especially Cd, up to 7.3.Through principal component analysis of major elements and heavy metals, it is concluded that heavy metals of municipal source stem from the erosion of road surface and inner pipeline in cities, heavy metals of mine source come from the mining and the leaching of tailings, heavy metals of industrial source are mostly generated by mechanical debris and metal dissolution, heavy metals of port sources are mainly from the transport ships and the intensive gas emissions from vehicles. The ecological risks of these sediments were evaluated with the Hakanson ecological risk index. It is concluded that the single factors of the ecological hazards for metals are Cd > Cu > Pb > Cr > Zn, the comprehensive index of potential ecological risks for metals from different sources decrease with port source > industrial source > mine source > municipal source.